Page 1 of 2 12 LastLast
Results 1 to 10 of 19

Thread: Revision of date of A00

  1. #1
    Legacy Account
    Posts
    7,362
    Sex
    Location
    United Kingdom
    Nationality
    British
    mtDNA
    H

    United Kingdom

    Revision of date of A00

    Eran Elhaik et al., The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome, European Journal of Human Genetics (2014) 22, 1111–1116.

    http://www.nature.com/ejhg/journal/v...g2013303a.html

    Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338 000 years ago (95% CI=237 000–581 000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100 000 years older than the earliest fossils of anatomically modern humans. This estimate raises two astonishing possibilities, either the novel Y chromosome was inherited after ancestral humans interbred with another species, or anatomically modern Homo sapiens emerged earlier than previously estimated and quickly became subdivided into genetically differentiated subpopulations. We demonstrate that the TMRCA estimate was reached through inadequate statistical and analytical methods, each of which contributed to its inflation. We show that the authors ignored previously inferred Y-specific rates of substitution, incorrectly derived the Y-specific substitution rate from autosomal mutation rates, and compared unequal lengths of the novel Y chromosome with the previously recognized basal lineage. Our analysis indicates that the A00 lineage was derived from all the other lineages 208 300 (95% CI=163 900–260 200) years ago.
    This paper was online 22 January 2014, so it may have been mentioned somewhere in the forum before.

  2. The Following 5 Users Say Thank You to Jean M For This Useful Post:

     Brent.B (08-16-2014),  Ezana (08-16-2014),  Mehrdad (08-15-2014),  MitchellSince1893 (04-16-2015),  Muircheartaigh (08-14-2014)

  3. #2
    Registered Users
    Posts
    129
    Sex
    Omitted
    Y-DNA
    F0R1a1a-Z280
    mtDNA
    R0H5B1

    Poland Slovakia Scotland England Ireland
    Okay how many times farther am I from A00 than E1b1b or C-V20 ? It has to be less than or equal to 3 for the age of A00 to be this young.
    Last edited by venustas; 08-15-2014 at 11:22 PM.
    Maternal Uncle y-line= F0R1b1-L21

  4. #3
    Registered Users
    Posts
    925
    Sex
    Omitted
    Location
    Colorado, USA
    mtDNA
    U5a2a1

    Quote Originally Posted by Jean M View Post
    Eran Elhaik et al., The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome. This paper was online 22 January 2014, so it may have been mentioned somewhere in the forum before.

    There has been some discussion of this paper, and in my opinion it offers nothing new other than arguing that there is uncertainty in mutation rates, and if you assume a different mutation rate you get a different age estimate. I'm amazed that this paper passed peer review. In some of the media at the the time of publication, Elhaik and crew made irrational statements about the findings in the original paper. I'm curious to know if Elhaik has done any serious scholarship as the two papers I've seen are shoddy research and seem to be more about self promotion than science.

  5. The Following 2 Users Say Thank You to GailT For This Useful Post:

     AJL (08-18-2014),  Jean M (08-16-2014)

  6. #4
    Gold Class Member
    Posts
    2,638
    Sex

    Quote Originally Posted by GailT View Post
    Elhaik and crew made irrational statements about the findings in the original paper.
    Take a look at this popular science article about the paper. The alleged quote from Dr. Elhaik is such outrageously absurd gibberish as to indicate that he doesn't understand the subject matter at all. If the quote is genuine, of course.
    ---
    “In fact, their [Krahn Karafet Hammer et al.] hypothesis creates a sort of space-time paradox whereby the most ancient individual belonging to Homo sapiens species has not yet been born. If we take the numerical results from previous studies seriously we can conclude that the past may be altered by the mother of Adam deciding not to conceive him in the future, thus, bringing a retroactive end to our species.”
    ---

  7. The Following 2 Users Say Thank You to lgmayka For This Useful Post:

     AJL (08-18-2014),  GailT (08-16-2014)

  8. #5
    Registered Users
    Posts
    87
    Sex
    Location
    Xanadu
    Ethnicity
    Ethiopian-American
    Y-DNA
    J1c2
    mtDNA
    L3i2

    United States of America Ethiopia
    Great article, Jean!

    lgmayka, I think that quotation is merely a way to demonstrate the extent to which the numbers are in disagreement with the current scientific consensus.

    These studies are very important for advancing scientific knowledge. There are literally millions of scientific papers published each year, many of dubious quality (ignoring the merit of their subject). Peer-review is supposed to weed out experiments not worthy of publication, but it's far from perfect. And in this "publish or die" environment that researchers must exist in, it's often inadequate for dealing with the sheer volume presented.

    Here are some good quotes from the paper for those without access. In particular, the mutation rate and generation time they used was questionable. They assumed a very low mutation rate based on a study of Icelandic families with autistic or schizophrenic children and a very high generation time of 20-40 years (when even today it's more like 25 years in the developed world and much lower in countries with worse access to healthcare).

    Here, we reassess the data and methodology in Mendez et al.2 In particular, we discuss (1) the decision to derive the Y-specific substitution rate from autosomal mutation rates instead of using previously inferred Y-specific substitution rates; and (2) the use of sequences of unequal lengths in the comparison between A00 and the previously recognized basal lineage, A0.

    We uncover several methodological irregularities and analytical biases, each of which, have inflated the TMRCA estimate. By correcting these, we infer the new Y lineage characterized by Mendez et al2 to be significantly younger than originally reported.
    (1) The decision to derive the Y-specific substitution rate from autosomal mutation rates instead of using previously inferred Y-specific substitution rates


    ...

    In their study, Mendez et al2 could have used existing estimates for Y-specific substitution rates in the literature.4, 13, 14 Instead, they derived a substitution rate for the Y chromosome (6.12 × 10−10) using autosomal mutation rates reported from an Icelandic data set of parent-offspring trios in which one child is either autistic or schizophrenic.15 Interestingly, the authors even acknowledge that the TMRCA would have been much shorter had they used the Y-specific mutation rate in the literature. For example, Xue et al13 sequenced approximately 10.15 Mb from two Y chromosomes of two European individuals separated by 13 generations and inferred a substitution rate of 1 × 10−9 substitutions per nucleotide per year, under the assumption that the generation time is 30 years. This estimate is consistent with estimates derived from human-chimpanzee Y chromosome analyses (1.5 × 10−9−2.1 × 10−9 substitutions per nucleotide per year) under the assumption of a divergence time range of 5–7 million years.16, 17

    A substitution rate estimate of 1 × 10−9 substitutions per nucleotide per year is a widely accepted estimate. For example, Wei et al18 applied this rate to estimate that the time depth of the Y-chromosomal tree was ~101 000–115 000 years, and dated the lineages found outside Africa to 57 000–74 000 years. Cruciani et al3 also applied this substitution rate to derive an estimate of ~142 000 years to the TMRCA of the Y chromosome.
    Substitution rate on the Y chromosome is not linearly related to the autosomal rate

    ...

    Although male mutation bias may explain most of the differences in the substitution rates between each sex chromosome and the autosomes, it cannot account for all of the rate variation; the magnitude of male mutation bias will vary significantly depending on which pair of chromosome types are compared.19, 20, 21 If estimates of male mutation bias vary depending on which chromosome types are compared, then factors other than replication must affect mutation rates on each chromosome type, and one cannot assume a direct correlation between the mutation rates of any chromosome types, as did Mendez et al.2

    The assumption that mutation rates are equal to substitution rates Mutation rate refers to the rate at which changes in the nucleotides are incorporated into the DNA sequence during replication, that is, the probability that an allele differs from the copy of that in its parent from which it was derived. Substitution rate refers to the rate at which a newly arisen allele is incorporated into a population, for example, when a newly arisen allele becomes fixed in a population. This rate is equal to experimentally measured apparent mutation rates only for fairly short times when recurring mutations, purifying selection, and genetic drift are negligible. Otherwise, those effects should be considered and corrected.

    The use of unreasonable generation times To obtain a mean substitution rate for the Y chromosome per generation (μy) of 6.12 × 10−10 with a range of 4.39 × 10−10 ≤ μy≤7.07 × 10−10, Mendez et al2 assumed that anatomically modern human (AMH) males had a paternal generation time that, on average, ranged from 20 to 40 years. This assumption is extremely important (and problematic) since it affects estimates of the male mutation bias.

    ...

    For instance, even among developed nations, where age at conception is delayed, generation times ranges from 20 to 30 years35 and stands at ~25 in the US.36 Less developed nations exhibit much shorter generation times (in the low 20 s).35 For the vast majority of human history and until the modern era, women married anytime from their mid- to late-teens and likely had their first child by the age of 20.37 Ancient societies were almost as age demanding for males. The Augustan marriage laws, for example, penalized males who did not sire a child by the age of 25.38 It thus seems unlikely that the average age of ancestral human fathers was older than, or even equal to, modern humans, particularly due to the fact that the mean life expectancy of Cameroon males (37.2 years) was lower than the purported upper bound of the generation time.39 By using a lower bound of 20 years, an average of 30 years, and an upper bound of 40 years, Mendez et al2 reduced the number of generations per unit time, and further inflated the TMRCA estimate.

    The study points out a few more examples of poor study design, but I just want to point out one more that's troubling and easy to make when you're a researcher looking for significance and novelty. It's easy to bias your data (in collection or processing), even if your analytical techniques are completely unbiased:

    (2) The use of sequences of unequal lengths in the comparison between A00 and the previously recognized basal lineage, A0
    Mendez et al2 sequenced a portion of Perry’s Y chromosome (A00) as well as the closest phylogenetic Y haplotype to identify private and derived mutations in this lineage. Interestingly, the authors counted mutations in ~240 kb of the X-degenerate portion of the A00 chromosome, but only reported mutations for ~180 kb of the A0 chromosome. We first note that a reliable evolutionary estimate cannot be obtained from 2% of the male-specific portion of the Y chromosome. Second, it is also unclear why the sequence of the previously known basal lineage is 25% shorter than the novel Y chromosome, given the author’s obvious intent to compare the two chromosomes. In fact, the A0 chromosome was originally sequenced to the full extent of the A00 chromosome, but the authors chose to omit 60 000 bases of it because they consist of ‘a large amount of mutations’ (FLM personal communication). Remarkably, they reported the mutations in the regions on the A00 chromosome for which the matching A0 regions were dropped. In Figure 1 and Supplementary Table S1 of Mendez et al,2 43 mutations were reported as derived for the A00 chromosome and 45 were A0 derived mutations. These mutations were divided into two types: A0T (18 mutations) in which A00 is the only ancestral lineage and A0 (27 mutations) mutations that are observed only in chromosomes that are in the A0 haplogroup, though some of these mutations may be absent from some A0 Y chromosomes. We believe that matching chromosomal regions should be compared instead of eliminating particular regions in an attempt to make the data fit a preconceived model. We further speculate that omitting regions for one lineage, but including them for another may have reduced their estimated age. Indeed, in our calculations below, we show that the TMRCA calculation using equivalent regions of A0 and A00 yields a much lower estimate than that reported by Mendez et al.2

    Again, it's my belief that these types of reviews are essential to continued scientific progress. It's great that there's an ever-increasing volume of scientific publications and knowledge being acquired, but it's important to always be skeptical and to carefully consider the validity of the methodology and data being presented. Science is hard. We, as humans, are inherently biased toward novelty and pattern recognition. Overcoming that bias is one of the hardest parts of being a good scientist, but it's necessary in order to not simply reaffirm our biases but actually uncover new information.

  9. #6
    Gold Class Member
    Posts
    2,638
    Sex

    A response to Elhaik et al. is reportedly "in press":
    ---
    Mendez, F.L., Veeramah, K.R., Thomas, M.G., Karafet, T.M., Hammer, M.F. Reply to 'The 'extremely ancient' chromosome that isn't by Elhaik et al' . (2014) EJHG in press.
    ---

  10. The Following 2 Users Say Thank You to lgmayka For This Useful Post:

     AJL (08-18-2014),  Ezana (08-17-2014)

  11. #7
    Gold Class Member
    Posts
    2,638
    Sex

    Quote Originally Posted by lgmayka View Post
    The alleged quote from Dr. Elhaik is such outrageously absurd gibberish as to indicate that he doesn't understand the subject matter at all. If the quote is genuine, of course.
    The quote is genuine. It appears on the web site of his own university, accompanied by scathing categorizations of this and other work of Dr. Hammer, including a comparison with modern cinematic fiction.
    ---
    Debunking unscientific theories is not new to Dr Elhaik. Earlier this year he debunked Hammer’s previous work on the unity of the Jewish genome...
    ...
    Dr Elhaik added: “We have shown that the University of Arizona study lacks any scientific merit."
    ...
    “Think of the movie Back to the Future, when Marty was worried that his parents would not meet and as a result he wouldn’t be born – it’s the same idea."

    ---

    It is certainly reasonable to debate the appropriate long-term mutation rate and generation span to apply to the human Y chromosome; and in fact, when the "Extremely ancient" paper by Hammer et al. first appeared, many of us suggested that certain parameters appeared to be chosen so as to stretch the age of Y-Adam as far back as possible.

    But Dr. Elhaik's incomprehensible illogic, and his acrimonious disparagement of an indisputably important discovery (of the A00 haplogroup), severely undermine his own credibility.
    Last edited by lgmayka; 08-16-2014 at 07:14 PM.

  12. The Following 2 Users Say Thank You to lgmayka For This Useful Post:

     AJL (08-18-2014),  GailT (07-31-2015)

  13. #8
    Registered Users
    Posts
    925
    Sex
    Omitted
    Location
    Colorado, USA
    mtDNA
    U5a2a1

    Elhaik arguments for the number of years per generation are based on Augustan marriage laws and mean life expectancy of Cameroon males. This has no relevance to estimating years per generation for the vast majority of human of history. So this critique is especially flawed.

  14. The Following User Says Thank You to GailT For This Useful Post:

     AJL (08-18-2014)

  15. #9
    Gold Class Member
    Posts
    2,638
    Sex

    Quote Originally Posted by GailT View Post
    Elhaik arguments for the number of years per generation are based on Augustan marriage laws and mean life expectancy of Cameroon males. This has no relevance to estimating years per generation for the vast majority of human of history.
    I see a more profound problem with Elhaik's generation argument. He is assuming that the correct generation span is the average father-to-son time interval across the entire human race. Wrong. For the calculation we are making, the correct generation span is the father-to-son time interval of the one patrilineal line that has survived since Y-Adam--in other words, the single most successful human patrilineage in the (pre) history of the human race. In general across its lifespan, this patrilineage must have belonged to the most reproductively successful men of their time. Such men probably continued to reproduce well into middle age, even if other men of their time did not.
    Last edited by lgmayka; 08-17-2014 at 10:14 AM.

  16. The Following User Says Thank You to lgmayka For This Useful Post:

     AJL (08-18-2014)

  17. #10
    Legacy Account
    Posts
    7,362
    Sex
    Location
    United Kingdom
    Nationality
    British
    mtDNA
    H

    United Kingdom
    Quote Originally Posted by Ezana View Post
    Great article, Jean!
    I had nothing to do with it.

Page 1 of 2 12 LastLast

Similar Threads

  1. Replies: 242
    Last Post: 05-22-2014, 03:08 PM
  2. Geno 2.0 raw date for haplotype 35 samples
    By DebbieK in forum R1b Early Subclades
    Replies: 0
    Last Post: 07-17-2013, 04:57 PM
  3. Replies: 0
    Last Post: 07-17-2013, 04:55 PM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •